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Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya
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Otieno, Grieven P., Murunga, Nickson, Agoti, Charles N., Gallagher, Katherine E., Awori, Juliet O. and Nokes, D. James (2020) Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya. Wellcome Open Research, 5 . 150. doi:10.12688/wellcomeopenres.16037.2
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WRAP-surveillance-endemic-human-coronaviruses-(HCoV-NL63-OC43-229E)-associated-childhood-pneumonia-Kilifi-Kenya-Nokes-2020.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (2043Kb) | Preview |
Official URL: http://dx.doi.org/10.12688/wellcomeopenres.16037.2
Abstract
Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya.
Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity.
Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one of the HCoV types surveyed in the study. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection. Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was was no change in the proportion infected by age. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified.
Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into their potential future burden and epidemiological characteristics.
| Item Type: | Journal Article | |||||||||||||||
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| Subjects: | Q Science > QR Microbiology > QR355 Virology | |||||||||||||||
| Divisions: | Faculty of Science > Life Sciences (2010- ) | |||||||||||||||
| Library of Congress Subject Headings (LCSH): | Coronaviruses, Pneumonia in children -- Kenya, Pneumonia | |||||||||||||||
| Journal or Publication Title: | Wellcome Open Research | |||||||||||||||
| Publisher: | F1000Research | |||||||||||||||
| ISSN: | 2398-502X | |||||||||||||||
| Official Date: | 22 September 2020 | |||||||||||||||
| Dates: |
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| Date of first compliant deposit: | 18 November 2020 | |||||||||||||||
| Volume: | 5 | |||||||||||||||
| Article Number: | 150 | |||||||||||||||
| DOI: | 10.12688/wellcomeopenres.16037.2 | |||||||||||||||
| Status: | Peer Reviewed | |||||||||||||||
| Publication Status: | Published | |||||||||||||||
| Access rights to Published version: | Open Access | |||||||||||||||
| RIOXX Funder/Project Grant: |
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